I am using Swiss-PdbViewer to determine thestructure of a fluorescent protein with a sequence homology to knowfluorescent proteins, such as GFP and DsRed. The protein of interesthas four domains due to gene duplication. Based on this information Iam using DsRed as a model, since the structure of DsRed has beensolved and it is tetrameric. I would like to know if there is a wayfor me to add a linker to connect each of the DsRed in the tetramericstructure. I have added some hypothetical linker amino acids to the C-termial of one of the DsRed in the tetrameric structure; however, I amunable to connect the linker to the N-terminal of 2nd DsRed in thestructure. I have also utilized sequence based homology modeling, butthat only predicts structure for one of the domain relative to theknow fluorescent proteins. I have also used PredictProtein todetermine the structure of my protein, but I have been unable todetermine whether or not predicted linkers are long enough to give myprotein a classical tetrameric structure of a fluorescent protein. Iwould greatly appreciate any and all suggestions and advise regardingthis problem. Please let me know if this is not the correct place forthis sort of email and if that is the case, then please feel free todirect my email to an appropriate location.

In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The evolutions in motif identification and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. Anyway nice post..